Edited by: Anton F. Post, Coastal Resource Center, University of Rhode Island, USA
Reviewed by: Michael Rappe, University of Hawaii at Manoa, USA; Jens Georg, Universität Freiburg, Germany
*Correspondence: Mary Ann Moran
This article was submitted to Aquatic Microbiology, a section of the journal Frontiers in Microbiology
†Present Address: Andrew S. Burns, Department of Biology, Georgia Institute of Technology, Atlanta, USA
This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
In oligotrophic ocean waters where bacteria are often subjected to chronic nutrient limitation, community transcriptome sequencing has pointed to the presence of highly abundant small RNAs (sRNAs). The role of sRNAs in regulating response to nutrient stress was investigated in a model heterotrophic marine bacterium
Small non-coding RNAs are common regulators of gene expression in bacteria, including those in marine environments (Shi et al.,
Heterotrophic marine bacteria are the primary recyclers of organic matter in the ocean, making their regulation strategies during C and N limitation important facets of marine element cycles. They must respond quickly to heterogeneity in C and nutrient availability on the microscale (resulting from patchy distributions of phytoplankton cells and nutrient plumes) and macroscale (resulting from terrestrial inputs, upwelling events, and phytoplankton blooms) (Azam and Malfatti,
Several sRNAs are already known to be involved in bacterial regulation under C limitation. One of the first bacterial sRNAs discovered was Spot 42 in
Small RNAs involved in nitrogen metabolism have also been identified. sRNA NsiR4, discovered in the freshwater cyanobacterium
To better understand the role of sRNAs in cellular regulation of C and N limitation, we sequenced transcripts from
Samples of steady-state
Sequence data were mapped to the genome of
DNA probes to central regions of abundant sRNAs were designed using Primer 3 (Untergasser et al.,
For each exponential and stationary phase sample, 30 μg of total RNA was separated on a 7 M urea 6% polyacrylamide gel. The gel was electro-blotted onto a nylon membrane, and RNA was crosslinked to the membrane by UV light. Probes were denatured, then hybridized overnight in ULTRAHyb-Oligo hybridization buffer (Ambion, Austin, TX). Northern blotting was carried out using the Chemiluminescent Nucleic Acid Detection Kit (Pierce Biotechnology, Rockford, IL). The size of sRNAs were estimated by measuring the migration of standard and sample bands in ImageJ (Schneider et al.,
Reverse transcription quantitative PCR (RT-qPCR) was carried out using chemostat RNA for sRNAs that were detected by Northern blotting and/or were significantly differentially expressed in the transcriptome experiments (Table
cis1 | 197 | SPO0003 | Cell cycle control | Antisense | 1.18 | 0.812 | ||
cis2 | 153 | SPO0040 | ABC transporter, permease | Transport | Antisense | 1.91 | 0.276 | Yes |
cis3 | 151 | SPO0098 | Peptide/opine/nickel transporter, ATP-binding | Transport | Antisense | 1.57 | NA | |
cis4 | 131 | SPO0108 | Truncated transposase | Antisense | 1.19 | 0.829 | ||
cis5 | 277 | SPO0116 | Acetate kinase | Energy production | Antisense | 1.99 | 0.150 | |
cis7¶ | 162 | SPO0132 | Sensor His kinase/response regulator | Signal transduction | Antisense | 1.04 | 0.967 | |
cis8 | 127 | SPO0184 | Hypothetical protein | Antisense | 2.70 | 0.066 | Yes | |
cis9 | 134 | SPO0185 | Hypothetical protein | Antisense | 2.30 | NA | ||
cis10 | 280 | SPO0192 | Motility | Antisense | 1.63 | NA | ||
cis13 | 155 | SPO0328 | Hypothetical protein | Antisense | 1.67 | NA | ||
cis14 | 135 | SPO0411 | Hypothetical protein | Antisense | 1.07 | NA | ||
cis16 | 139 | SPO0560 | Oligopeptide ABC transporter, periplasmic | Transport | Antisense | −1.31 | NA | |
cis17 | 236 | SPO0574 | ABC transporter, ATP binding | Transport | Antisense | −1.37 | NA | |
cis18 | 197 | SPO0588 | Transcriptional regulator, LysR family | Transcriptional regulation | Antisense | 1.54 | NA | |
cis19 | 128 | SPO0603 | Hypothetical protein | Antisense | 1.02 | 0.985 | ||
− |
||||||||
cis22¶ | 218§ | SPO0628a | Hypothetical protein | Antisense | 1.12 | 0.788 | Yes | |
cis23 | 168 | SPO0649 | Sugar ABC transporter, permease | Transport | Antisense | −1.42 | 0.485 | |
cis25 | 175 | SPO0660 | Transport | Antisense | 1.42 | NA | ||
cis26 | 158 | SPO0680 | Glyoxylase family protein | Resistance | Antisense | 1.16 | NA | |
− |
||||||||
cis29 | 173 | SPO0708 | Cell-cell interaction | Antisense | 1.31 | NA | ||
cis31¶ | 332 | SPO0745 | Hypothetical protein | Antisense | 1.93 | 0.088 | ||
cis32 | 297 | SPO0749 | Hypothetical protein | Antisense | 1.31 | 0.789 | ||
cis34 | 136 | SPO0825 | Branched-chain amino acid transport, periplasmic | Transport | Antisense | 1.48 | NA | |
cis35¶ | 316 | SPO0882 | Hypothetical protein | Antisense | 1.29 | 0.657 | ||
cis36 | 187 | SPO0900 | Sulfate adenyltransferase | Ion metabolism | Antisense | −1.33 | 0.642 | |
cis37 | 188 | SPO0946 | Phosphomannomutase/glucomutase | Cell-cell interaction | Antisense | −1.13 | NA | |
cis39 | 161 | SPO1039 | Hypothetical protein | Antisense | 1.10 | NA | ||
cis40¶ | 251 | SPO1059 | Serine/threonine protein kinase | Signal transduction | Antisense | 1.07 | 0.919 | |
cis41 | 255 | SPO1176 | Serine/threonine protein phosphatase | Antisense | −1.47 | 0.608 | ||
cis47¶ | 164 | SPO1406 | Hypothetical protein | Antisense | 1.34 | 0.457 | ||
cis50¶ | 258 | SPO1572 | Serine hydroxymethyltranferase | Amino acid metabolism | Antisense | −1.40 | 0.549 | |
cis51 | 211 | SPO1633 | Hypothetical protein | Antisense | 1.64 | 0.084 | ||
cis52 | 179 | SPO1658 | Oligo/dipeptide ABC transporter, permease | Transport | Antisense | 1.73 | NA | Yes |
cis55¶ | 158 | SPO1929 | Peptidoglycan binding protein | Cell-cell interaction | Antisense | −1.19 | 0.813 | |
cis57¶ | 260 | SPO2024 | Aminotransferase | Antisense | 1.72 | 0.183 | ||
cis61 | 201 | SPO2297 | Hypothetical protein | Antisense | 1.34 | 0.604 | ||
− |
||||||||
cis68¶ | 413 | SPO2736 | Hypothetical protein | Antisense | −1.35 | 0.485 | ||
cis70¶ | 224 | SPO2940 | Serine hydroxymethyltransferase | Amino acid metabolism | Antisense | −1.40 | NA | |
cis71 | 186 | SPO2965 | Ribosomal protein L33 | Translation | Antisense | 2.50 | 0.091 | |
cis72 | 455 | SPO2994 | Peptide/nickel/opine transporter, periplasmic | Transport | Antisense | 1.62 | 0.479 | |
cis73¶ | 401 | SPO2022 | Valyl-tRNA synthetase | Translation | Antisense | 1.22 | 0.805 | |
cis74 | 173 | SPO3036 | Metallo-B-lactamase family | Cell-cell interaction | Antisense | 1.62 | NA | |
cis75¶ | 251 | SPO3039 | Polar AA ABC transporter, periplasmic | Transport | Antisense | 1.13 | 0.865 | |
cis76¶ | 178 | SPO3097 | 3-hydroxyisobutyrate dehydrogenase | Lipid metabolism | Antisense | 1.45 | 0.510 | |
cis77 | 163 | SPO3130 | Recombination and repair | Antisense | 1.19 | 0.806 | ||
cis78¶ | 217 | SPO3398 | Homocysteine S-methyltransferase | Amino acid metabolism | Antisense | 1.23 | NA | |
cis80¶ | 215 | SPO3455 | Adenylate/guanylate cyclase | Signal transduction | Antisense | 1.33 | 0.585 | |
cis84 | 129 | SPO3628 | GNAT family acetyltransferase | Antisense | 1.49 | 0.393 | ||
cis86 | 135 | SPO3666 | Oxidoreductase FAD-binding | Antisense | 1.09 | NA | ||
cis89¶ | 326§ | SPO3689 | Transcriptional regulator, MarR family | Transcriptional regulation | Antisense | 1.44 | 0.195 | Yes |
cis90¶ | 230§ | SPO3787 | sugar ABC transporter, periplasmic | Transport | Antisense | 1.30 | 0.493 | Yes |
cis92 | 148 | SPOA0008 | Hypothetical protein | Antisense | 1.86 | NA | ||
cis93¶ | 221 | SPOA0011 | S-adenosylmethionine synthase | Coenzyme metabolism | Antisense | −1.07 | NA | |
− |
||||||||
cis95¶ | 180 | SPOA0082 | Hypothetical protein | Antisense | 1.21 | 0.749 | ||
cis97 | 245 | SPOA0121 | Sulfatase family protein | Antisense | −1.06 | 0.944 | ||
cis99 | 404 | SPOA0269 | Hypothetical protein | Antisense | 2.26 | NA | ||
cis102 | 143 | SPOA0342 | Hypothetical protein | Antisense | −1.34 | 0.637 | ||
cis103 | 207 | SPOA0347 | Hypothetical protein | Antisense | −1.38 | 0.604 | ||
cis104 | 203 | SPOA0433 | Putative esterase | Antisense | 1.49 | NA | ||
riboswitch82 | 188 | SPO1974 | LuxR family autoinducer-binding regulator | Transcription | Antisense | −1.06 | 0.986 | |
4.5S RNP¶ | 177§ | SPO1399 | Translation | Rfam | NA | NA | Yes | |
A metabolic network of
A total of 99 uncharacterized sRNAs were found in
Differential expression of sRNAs from C- and N-limited chemostat cultures was used to identify sRNAs potentially involved in nutrient-specific responses. A total of 14% of the sRNAs (14 out of 99) were differentially expressed between the two conditions compared with 10% of the 4252 protein coding genes in the transcriptome (Chan et al.,
To independently confirm the presence and size of sRNAs identified by transcriptome sequencing, Northern blotting was conducted for 11 abundant sRNAs. This analysis was carried out on cells grown to exponential phase (non-limiting conditions) and stationary phase (limiting conditions) because of constraints in the amount of RNA available from the chemostats. Blotting under these different conditions confirmed the presence of 8 of the sRNAs, most of which were present at higher levels in stationary phase cells compared to exponentially growing cells (Figure
A previous analysis of transcription patterns of protein-encoding genes during
The functional category with the highest number of genes opposite the 69
The next largest functional category of genes antisense to
Other functional categories of genes antisense to
Target gene prediction is more challenging for
trans6 | 101 | SPO0684 | Glyoxylase family protein | Resistance | 0.000 | |
SPO1441 | Fatty acid desaturase family protein | Lipid metabolism | 0.000 | |||
SPO3188 | Hypothetical protein | 0.001 | ||||
SPO3394 | GDSL-like lipase/acylhydrolase, putative | Lipid metabolism | 0.002 | |||
SPO2054 | Cytochrome c oxidase assembly protein | Energy production | 0.004 | |||
SPO2735 | Type I restriction-modification system, R subunit | Nucleic acid metabolism | 0.004 | |||
SPO0765 | Glutamine synthetase family protein | Amino acid metabolism | 0.005 | |||
SPO3739 | Hydantoinase/oxoprolinase family protein | Amino acid metabolism | 0.007 | |||
SPO1134 | NnrU family protein | 0.009 | ||||
SPO1906 | Hypothetical protein | 0.009 | ||||
SPO2498 | 2′-deoxycytidine 5′-triphosphate deaminase | Nucleic acid metabolism | 0.009 | |||
SPO2912 | MerR family transcriptional regulator | Transcriptional regulator | 0.009 | |||
SPO3245 | Nicotinate-nucleotide pyrophosphorylase | Coenzyme metabolism | 0.009 | |||
trans11 | 189 | SPO0657 | Coenzyme metabolism | 0.003 | ||
SPO1108 | DnaJ-like protein DjlA, putative | Post-translational modification | 0.003 | |||
SPO3602 | Hypothetical protein | 0.007 | ||||
trans15 | 225 | SPO0298 | acyl-CoA dehydrogenase family protein | Lipid metabolism | 0.001 | |
SPO0568 | 2-oxoacid ferredoxin oxidoreductase | Amino acid metabolism | 0.001 | |||
SPO2180 | Hypothetical protein | 0.002 | ||||
SPO0940 | Hypothetical protein | 0.005 | ||||
SPO3617 | Peptidoglycan-binding protein, putative | Cell-cell interaction | 0.005 | |||
SPO1609 | Polyamine ABC transporter, ATP-binding | Transport | 0.008 | |||
SPO0831 | Xanthine dehydrogenase family, medium subunit | Nucleic acid metabolism | 0.009 | |||
SPO0937 | Hypothetical protein | 0.009 | ||||
trans21 | 264 | SPO1144 | Universal stress protein family protein | 0.003 | ||
SPO2761 | Pantothenate kinase | Coenzyme metabolism | 0.004 | |||
SPO0685 | Fumarylacetoacetase | Amino acid metabolism | 0.005 | |||
SPO2385 | Benzaldehyde lyase, putative | 0.007 | ||||
trans28 | 161 | SPO0858 | Methylamine utilization protein MauG, putative | 0.000 | ||
SPO0381 | Protease, putative | Protein degradation | 0.001 | |||
SPO0129 | T4 family peptidase | Protein degradation | 0.004 | |||
SPO1697 | Aminotransferase, classes I and II | Amino acid metabolism | 0.006 | |||
SPO0934 | Hypothetical protein | 0.007 | ||||
SPO0328 | Hypothetical protein | 0.009 | ||||
trans30 | 201 | N/A | ||||
trans33 | 111 | SPO0185 | Hypothetical protein | 0.000 | ||
SPO2572 | Hypothetical protein | 0.001 | ||||
SPO2073 | Hypothetical protein | 0.004 | ||||
SPO0583 | LysR family transcriptional regulator | Transcriptional regulator | 0.005 | |||
SPO2679 | Short chain oxidoreductase | 0.006 | ||||
SPO2900 | tRNA 2-selenouridine synthase | Translation and biogenesis | 0.007 | |||
SPO3172 | Hypothetical protein | 0.007 | ||||
SPO0759 | Hypothetical protein | 0.008 | ||||
SPO0872 | Polysaccharide deacetylase family protein | Carbohydrate metabolism | 0.009 | |||
SPO1845 | Oxidoreductase, molybdopterin-binding | 0.009 | ||||
trans38 | 311 | SPO1267 | MarR family transcriptional regulator | Transcriptional regulation | 0.001 | |
SPO2455 | Organic solvent tolerance protein, putative | Membrane protein | 0.002 | |||
SPO1286 | Hypothetical protein | 0.004 | ||||
SPO3027 | Histidinol-phosphate aminotransferase | Amino acid metabolism | 0.005 | |||
SPO1199 | Hypothetical protein | 0.008 | ||||
SPO3633 | Molybdopterin converting factor, subunit 2 | Coenzyme metabolism | 0.008 | |||
SPO1311 | Renal dipeptidase family protein | Protein degradation | 0.009 | |||
SPO2536 | LuxR family transcriptional regulator | Transcriptional regulation | 0.009 | |||
trans42 | 143§ | SPO3876 | Hypothetical protein | 0.009 | No | |
trans44 | 265§ | SPO0873 | Ureidoglycolate hydrolase | Nucleic acid metabolism | 0.003 | Yes |
SPO1532 | Hypothetical protein | 0.005 | ||||
SPO0005 | Hypothetical protein | 0.008 | ||||
SPO1350 | Hypothetical protein | 0.009 | ||||
trans45¶ | 351 | SPO3050 | Hypothetical protein | 0.003 | ||
SPO2852 | CzcN domain-containing protein | 0.003 | ||||
SPO2542 | Biotin/lipoate binding domain-containing protein | Coenzyme metabolism | 0.006 | |||
SPO2703 | Hypothetical protein | 0.008 | ||||
SPO2977 | Adenylate/guanylate cyclase | Signal transduction | 0.008 | |||
SPO3862 | Putative lipoprotein | Cell wall/membrane | 0.009 | |||
trans46 | 141 | SPO3330 | Ribonuclease R | Translation and biogenesis | 0.001 | |
SPO2342 | Hypothetical protein | 0.004 | ||||
SPO1399 | AraC family transcriptional regulator | Transcriptional regulation | 0.006 | |||
SPO3662 | Hypothetical protein | 0.008 | ||||
SPO2067 | Hypothetical protein | 0.010 | ||||
SPO2790 | Methylcrotonyl-CoA carboxylase, beta subunit | Lipid metabolism | 0.010 | |||
SPO3333 | Hypothetical protein | 0.010 | ||||
trans48¶ | 142 | SPO1762 | 6,7-dimethyl-8-ribityllumazine synthase | Coenzyme metabolism | 0.004 | |
SPO1508 | Quinoprotein ethanol dehydrogenase | 0.005 | ||||
SPO3019 | Xanthine dehydrogenase family, large subunit | Nucleic acid metabolism | 0.006 | |||
SPO1029 | YeeE/YedE family protein | 0.007 | ||||
trans49 | 124 | SPO1050 | Phage integrase family site specific recombinase | Phage | 0.001 | |
SPO0323 | Hypothetical protein | 0.001 | ||||
SPO0526 | Acetylglutamate kinase | Amino acid metabolism | 0.002 | |||
SPO3390 | Hypothetical protein | 0.003 | ||||
SPO2630 | C4-dicarboxylate transport sensor protein | Transport | 0.006 | |||
SPO1884 | Methionine synthase I | Amino acid metabolism | 0.009 | |||
SPO3077 | TldD/PmbA family protein | 0.009 | ||||
SPO1050 | Phage integrase family site specific recombinase | Phage | 0.001 | |||
SPO0323 | Hypothetical protein | 0.001 | ||||
trans54 | 207 | N/A | ||||
trans56 | 146 | SPO0201 | Hypothetical protein | 0.001 | ||
SPO1217 | DNA-binding protein, putative | Transcriptional regulation | 0.001 | |||
SPO0547 | Hypothetical protein | 0.002 | ||||
SPO1032 | Hypothetical protein | 0.006 | ||||
SPO2286 | Autoinducer-binding regulator LuxR | Transcriptional regulation | 0.007 | |||
SPO0201 | Hypothetical protein | 0.001 | ||||
trans58 | 141 | SPO3492 | Hypothetical protein | 0.000 | ||
SPO2182 | Permease, putative | Transport | 0.001 | |||
SPO0236 | Glycerophosphoryl diester phosphodiesterase putative | Lipid metabolism | 0.001 | |||
SPO0950 | Uracil-DNA glycosylase, putative | Nucleic acid metabolism | 0.001 | |||
SPO3756 | OmpA domain-containing protein | Cell wall/membrane | 0.004 | |||
SPO1732 | Single-stranded-DNA-specific exonuclease RecJ | Recombination and repair | 0.005 | |||
SPO0965 | Acetyltransferase | 0.006 | ||||
SPO1596 | Hypothetical protein | 0.006 | ||||
SPO0846 | Phosphopantetheinyl transferase PptA, putative | Coenzyme metabolism | 0.008 | |||
SPO1099 | Hypothetical protein | 0.010 | ||||
trans59¶ | 124 | N/A | ||||
trans62¶ | 225§ | SPO0491 | Hypothetical protein | 0.001 | Yes | |
SPO2176 | Hypothetical protein | 0.003 | ||||
SPO2943 | Alpha/beta fold family hydrolase | 0.004 | ||||
SPO2635 | Phosphoadenosine phosphosulfate reductase | Sulfur metabolism | 0.004 | |||
SPO2397 | Carbon monoxide dehydrogenase, large subunit | 0.005 | ||||
SPO2759 | NUDIX family hydrolase | Nucleic acid metabolism | 0.005 | |||
SPO0294 | NUDIX family hydrolase | Nucleic acid metabolism | 0.007 | |||
SPO0571 | PKD domain-containing protein | 0.007 | ||||
SPO1376 | Glycosyl transferase, group 2 family protein | Carbohydrate metabolism | 0.008 | |||
SPO2218 | Excinuclease ABC subunit A | Recombination and repair | 0.008 | |||
SPO2718 | Hypothetical protein | 0.008 | ||||
SPO2640 | XdhC/CoxI family protein | Nucleic acid metabolism | 0.009 | |||
SPO3493 | Transporter, putative | Transport | 0.009 | |||
trans63¶ | 488 | SPO0331 | Thiol:disulfide interchange protein, putative | 0.000 | ||
SPO0965 | Acetyltransferase | 0.002 | ||||
SPO3587 | Hypothetical protein | 0.004 | ||||
SPO1527 | Hypothetical protein | 0.005 | ||||
SPO2008 | Polyamine ABC transporter, permease protein | Transport | 0.009 | |||
SPO0305 | AzlC family protein | Amino acid metabolism | 0.010 | |||
SPO0773 | Acetyl-CoA acyltransferase/thiolase family | Lipid metabolism | 0.010 | |||
SPO2147 | Hypothetical protein | 0.010 | ||||
trans65 | 295 | SPO1043 | Hypothetical protein | 0.000 | ||
SPO3750 | Hypothetical protein | 0.001 | ||||
SPO2911 | Thioesterase family protein | 0.003 | ||||
SPO2543 | GntR family transcriptional regulator | Transcriptional regulation | 0.004 | |||
SPO2551 | Peptide/opine/nickel uptake ATP-binding protein | Transport | 0.008 | |||
SPO0919 | MarR family transcriptional regulator | Transcriptional regulation | 0.009 | |||
trans66 | 130 | SPO0164 | Oxidoreductase, FMN nucleotide-disulfide | 0.003 | ||
SPO1125 | Hypothetical protein | 0.006 | ||||
SPO1226 | Putative lipoprotein | Lipid metabolism | 0.006 | |||
SPO1510 | Efflux ABC transporter, permease protein | Transport | 0.007 | |||
SPO3172 | Hypothetical protein | 0.009 | ||||
trans69 | 160§ | SPO0934 | Hypothetical protein | 0.007 | Yes | |
SPO3650 | Adenylate/guanylate cyclase | Signal transduction | 0.009 | |||
trans79 | 436 | SPO3223 | Response regulator | Transcriptional regulation | 0.002 | |
SPO1656 | Oligopeptide/dipeptide ABC, ATP-binding | Transport | 0.003 | |||
SPO0310 | Molybdopterin biosynthesis protein MoeA | Coenzyme metabolism | 0.004 | |||
SPO1432 | Rhodanese domain-containing protein | 0.006 | ||||
SPO0078 | Ribosomal subunit interface protein, putative | Translation and biogenesis | 0.007 | |||
SPO2314 | DsbE periplasmic thiol:disulfide oxidoreductase | Post-translational modification | 0.007 | |||
trans83 | 121 | SPO1889 | Alcohol dehydrogenase, zinc-containing | 0.002 | ||
SPO0829 | Hypothetical protein | 0.002 | ||||
SPO2580 | Hypothetical protein | 0.003 | ||||
SPO1905 | Fumarate hydratase | Energy production | 0.004 | |||
SPO2296 | Hypo#thetical protein | 0.006 | ||||
SPO0451 | D-alanyl-D-alanine carboxypeptidase | Amino acid metabolism | 0.007 | |||
SPO1189 | Hypothetical protein | 0.007 | ||||
SPO1273 | FAD-dependent thymidylate synthase | Nucleic acid metabolism | 0.007 | |||
SPO2196 | Diaminopropionate ammonia-lyase | Amino acid metabolism | 0.007 | |||
SPO2407 | ISSpo6, transposase orfB | Recombination and repair | 0.007 | |||
trans85¶ | 116 | SPO0295 | Hypothetical protein | 0.003 | ||
SPO2757 | EF hand domain-containing protein | 0.007 | ||||
trans87¶ | 150 | SPO1856 | ribonuclease BN, putative | Translation and biogenesis | 0.009 | |
SPO3851 | HemY domain-containing protein | Coenzyme metabolism | 0.009 | |||
trans91¶ | 201 | SPO0387 | Hypothetical protein | 0.002 | ||
SPO2407 | ISSpo6, transposase orfB | Recombination and repair | 0.009 | |||
trans98 | 337 | SPO0220 | rRNA large subunit methyltransferase | 0.001 | ||
SPO3402 | Amino acid transporter LysE | Transport | 0.002 | |||
SPO1802 | Hypothetical protein | 0.003 | ||||
SPO1481 | Hypothetical protein | 0.003 | ||||
SPO2249 | Hypothetical protein | 0.005 | ||||
SPO0879 | acyl-CoA dehydrogenase family protein | Lipid metabolism | 0.005 | |||
SPO3823 | 50S ribosomal protein L23 | Translation and biogenesis | 0.005 | |||
SPO3600 | Pyruvate kinase | Carbohydrate metabolism | 0.007 | |||
SPO1395 | AraC family transcriptional regulator | Transcriptional regulation | 0.010 | |||
trans100 | 201 | SPO0259 | Hypothetical protein | 0.000 | ||
SPO1198 | Hypothetical protein | 0.006 |
A non-coding RNA with homology to the 6S RNA was also found in the
sRNAs and their regulatory targets may or may not have positively correlated patterns of expression, depending on whether the sRNAs affect transcript stability or instead work at the level of translation, and whether they act as activators or repressors. To determine whether there was any consistency in sRNA mode of action, the fold-difference between C- and N-limiting conditions for predicted target genes was plotted against the fold-difference for their corresponding
We were interested in understanding whether sRNAs play more important roles in the regulation of central metabolism (typically encoded in the core genome) or the regulation of peripheral or non-core metabolic processes (encoded in the pan genome). A metabolic map based on the
Carbon and nitrogen limitation represent major challenges to the growth of heterotrophic bacteria and affect both anabolic and catabolic processes. Of the 14 sRNAs that showed significant differential regulation in the comparison between C and N limitation, most were higher under C limitation (10 of 14) (Table
Transporter genes made up the largest functional class of predicted target genes of
Two target genes that may work together in the synthesis and export of a toxin were predicted to be under the control of sRNAs (cis12 and cis24) (Table
Although not differentially transcribed, two
Thirty sRNAs identified here were also expressed by
The regulatory mechanisms of bacterial sRNA are typically based on direct RNA-RNA binding with a target mRNA, with some exceptions for sRNAs that interact with proteins (Gottesman and Storz,
sRNAs have the potential to participate in expansion of the functional capabilities of marine bacteria by facilitating regulation of genes acquired by horizontal transfer. They are less costly to maintain than protein regulators, and their regulatory abilities are encoded directly with the gene being transferred.
The results of this study emphasize the number and variety of sRNAs produced by a heterotrophic marine bacterium and the need for additional research into the role of sRNAs in facilitating ecological adaptations. sRNAs represent an additional layer of regulation governing the cycling of C and nutrients in the ocean that affects the interpretation of transcriptome data both in model organisms and marine microbial communities.
AR designed the project, conducted the research, and wrote the paper. AB designed the project, conducted the research, and wrote the paper. LC conducted the research. MM designed the project and wrote the paper.
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
This research was supported by NSF grants OCE1342694 and OCE1356010 and Gordon and Betty Moore Foundation grant GBMF538.01.
The Supplementary Material for this article can be found online at: