Sizing up metatranscriptomics

ISME Journal

Volumn 7, Issue 2, 2013, Pages 237-243

  Moran, Mary Ann ^a   Satinsky, Brandon ^a   Gifford, Scott M ^a,b   Luo, Haiwei ^a   Rivers, Adam ^a   Chan, Leong Keat ^a,c   Meng, Jun ^a   Durham, Bryndan P ^a   Shen, Chen ^a   Varaljay, Vanessa A ^a   Smith, Christa B ^a   Yager, Patricia L ^a   Hopkinson, Brian M ^a  

^a UNIVERSITY OF GEORGIA   (United States)

^b Massachusetts Institute of Technology Cambridge   (United States)

^c DOE JOINT GENOME INSTITUTE   (United States)

Author keywords

bacteria; macromolecules; metatranscriptomics; mRNA

Indexed keywords

BACTERIAL PROTEIN; BACTERIAL RNA; MESSENGER RNA; SEA WATER; TRANSCRIPTOME;

BACTERIUM; DATA SET; ENVIRONMENTAL CUE; GENE EXPRESSION; GENOMICS; MICROBIAL COMMUNITY; MICROBIAL ECOLOGY; RNA; SEAWATER;

BACTERIUM; GENETICS; HALF LIFE TIME; METAGENOMICS; MICROBIOLOGY; REVIEW;

BACTERIA; BACTERIAL PROTEINS; HALF-LIFE; METAGENOMICS; RNA, BACTERIAL; RNA, MESSENGER; SEAWATER; TRANSCRIPTOME; WATER MICROBIOLOGY;

BACTERIA (MICROORGANISMS);

EID: 84872965253     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2012.94     Document Type: Review

References (47)

1. Azam F, Malfatti F. (2007). Microbial structuring of marine ecosystems. Nat Rev Microbiol 5: 966-966.
2. Bernstein JA, Khodursky AB, Lin P-H, Lin-Chao S, Cohen SN. (2002). Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays. Proc Natl Acad Sci USA 99: 9697-9702.
3. Borek E, Ponticorvo L, Rittenberg D. (1958). Protein turnover in microorganisms. Proc Natl Acad Sci USA 44: 369-374.
4. Curson ARJ, Rogers R, Todd JD, Brearley CA, Johnston AWB. (2008). Molecular genetic analysis of a dimethylsulfoniopropionate lyase that liberates the climate-changing gas dimethylsulfide in several marine a-proteobacteria and Rhodobacter sphaeroides. Environ Microbiol 10: 757-767.
5. de Menezes A, Clipson N, Doyle E. (2012). Comparative metatranscriptomics reveals widespread community responses during phenanthrene degradation in soil. Environ Microbiol; e-pub ahead of print; doi:10.1111/j. 1462-2920.2012.02781.x. Dennis PP, Bremer H. (1974). Macromolecular composition during steady-state growth of Escherichia coli B/r. J Bact 119: 270-281.
6. Doney SC, Abbott MR, Cullen JJ, Karl DM, Rothstein L. (2004). From genes to ecosystems: the ocean's new frontier. Front Ecol Environ 2: 457-468.
7. Fenchel T. (2002). Microbial behavior in a heterogeneous world. Science 296: 1068-1071.
8. Gifford SM, Sharma S, Booth M, Moran MA. (2012). Expression patterns reveal niche diversification in a marine microbial assemblage. ISME J (in press).
9. Gifford SM, Sharma S, Rinta-Kanto JM, Moran M. (2011). Quantitative analysis of a deeply-sequenced marine microbial metatranscriptome. ISME J 5: 461-472.
10. Gilbert JA, Field D, Huang Y, Edwards R, Li W, Gilna P et al. (2008). Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities. PLoS One 3: e3042.
11. Giovannoni SJ, Tripp HJ, Givan S, Podar M, Vergin KL, Baptista D et al. (2005). Genome streamlining in a cosmopolitan oceanic bacterium. Science 309: 1242-1245.
12. Golding I, Paulsson J, Zawilski SM, Cox EC. (2005). Realtime kinetics of gene activity in individual bacteria. Cell 123: 1025-1036.
13. Gyaneshwar P, Paliy O, McAuliffe J, Popham DL, Jordan MI, Kustu S. (2005). Sulfur and nitrogen limitation in Escherichia coli K-12: specific homeostatic responses. J Bacteriol 187: 1074-1090.
14. Hambraeus G, von Wachefeldt C, Hederstedt L. (2003). Genome-wide survey of mRNA half-lives in Bacillus subtilis identifies extremely stable mRNAs. Mol Gen Genomics 269: 706-714.
15. Ingraham JL, Maaløe O, Neidhardt FC. (1983). The Growth of the Bacterial Cell. Sinauer Associates: Sunderland, MA.
16. Jørgensen BB. (2011). Deep subseafloor microbial cells on physiological standby. Proc Natl Acad Sci USA 108: 18193-18194.
17. Kaufmann BB, van Oudenaarden A. (2007). Stochastic gene expression: from single molecules to the proteome. Curr Opin Genet Dev 17: 107-112.
18. Koch AL, Levy HR. (1955). Protein turnover in growing cultures of Escherichia coli. J Biol Chem 217: 947-958.
19. Kolodrubetz D, Schleif R. (1981). Identification of AraC protein and two-dimensional gels, its in vivo instability and normal level. J Mol Biol 149: 133-139.
20. Kramer JG, Singleton FL. (1992). Variations in rRNA content of marine Vibrio spp. during starvationsurvival and recovery. Appl Environ Microbiol 58: 201-207.
21. Lauro FM, McDougald D, Williams TJ, Egan S, Rice S, DeMaere MZ et al. (2009). A tale of two lifestyles: the genomic basis of trophic strategy in bacteria. Proc Natl Acad Sci USA 106: 15527-15533.
22. Lee S, Fuhrman JA. (1987). Relationships between biovolume and biomass of naturally derived marine bacterioplankton. Appl Environ Microbiol 53: 1298-1303.
23. Lee S, Kemp PF. (1994). Single-cell RNA content of natural marine planktonic bacteria measured by hybridization with multiple 16S rRNA-targeted fluorescent probes. Limnol Oceanogr 39: 869-879.
24. Liu Z, Klatt CG, Wood JM, Rusch DB, Ludwig M, Wittekindt N et al. (2012). Metatranscriptomic analyses of chlorophototrophs of a hot-spring microbial mat. ISME J 5: 1279-1290.
25. Maier T, Gu ell M, Serrano L. (2009). Correlation of mRNA and protein in complex biological samples. FEBS Lett 583: 3966-3973.
26. Mandelstam J. (1957). Turnover of protein in growing and non-growing populations of Escherichia coli. Biochem J 6: 110-119.
27. McCarren J, Becker JW, Repeta DJ, Shi Y, Young CR, Malmstrom RR et al. (2010). Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea. Proc Natl Acad Sci USA 107: 16420-16427.
28. Neidhardt FC. (1996). Escherichia Coli and Salmonella: Cellular and Molecular Biology. ASM Press: Washington, DC.
29. Neidhardt FC, Umbarger HE. (1996). Chemical composition of Escherichia coli. In: Neidhardt FC, Curtiss R III, Ingraham JL, Lin ECC, Low KB, Magasanik B, Reznikoff WS, Riley M, Schaechter M, Umbarger HE (eds) Escherichia Coli and Salmonella Typhimurium: Cellular and Molecular Biology, 2nd edn. ASM Press: Washington, DC, pp 13-16.
30. Ovacik MA, Androulakis IP. (2008). On the potential for integrating gene expression and metabolic flux data. Curr Bioinform 3: 142-148.
31. Poretsky RS, Sun S, Mou X, Moran M. (2010). Transporter genes expressed by coastal bacterioplankton in response to dissolved organic carbon. Environ Microbiol 12: 616-627.
32. Price PB, Sowers T. (2004). Temperature dependence of metabolic rates for microbial growth, maintenance, and survival. Proc Natl Acad Sci USA 101: 4631-4636.
33. Raes J, Bork P. (2008). Molecular eco-systems biology: towards an understanding of community function. Nat Rev Microbiol 6: 693-699.
34. Riedel T, Tomasch J, Buchholz I, Jacobs J, Kollenberg M, Gerdts G et al. (2010). Constitutive expression of the proteorhodopsin gene by a flavobacterium strain representative of the proteorhodopsin-producing microbial community in the North Sea. Appl Environ Microbiol 76: 3187-3197.
35. Satinsky BM, Smith CB, Crump BC, Sharma S, Dougherty M, Fortunato C et al. Taking stock of the meta-ome: microbial gene transcription ratios in the Amazon River Plume (in preparation).
36. Schut F, De Vries EJ, Gottschal JC, Robertson BR, Harder W, Prins RA et al. (1993). Isolation of typical marine bacteria by dilution culture: growth, maintenance, and characteristics of isolates under laboratory conditions. Appl Environ Microbiol 59: 2150-2160.
37. Selinger DW, Saxena RM, Cheung KJ, Church GM, Rosenow C. (2003). Global RNA half-life analysis in Escherichia coli reveals positional patterns of transcript degradation. Genome Res 13: 216-223.
38. Shi Y, McCarren J, DeLong EF. (2012). Transcriptional responses of surface water marine microbial assemblages to deep-sea water amendment. Environ Microbiol 14: 191-206.
39. Simon M, Azam F. (1989). Protein content and protein synthesis rates of planktonic bacteria. Mar Ecol Prog Ser 51: 201-213.
40. Sowell SM, Wilhelm LJ, Norbeck AD, Lipton MS, Nicora CD, Barofsky DF et al. (2009). Transport functions dominate the SAR11 metaproteome at low-nutrient extremes in the Sargasso Sea. ISME J 3: 93-105.
41. Steglich C, Lindell D, Futschik M, Rector T, Steen R, Chisholm SW. (2010). Short RNA half-lives in the slow-growing marine cyanobacterium Prochlorococcus. Genome Biol 11: R54.
42. Steindler L, Schwalbach MS, Smith DP, Chan F, Giovannoni SJ. (2011). Energy starved Candidatus Pelagibacter ubique substitutes light-mediated ATP production for endogenous carbon respiration. PLoS One 6: e19725.
43. Stocker R, Seymour JR, Samadani A, Hunt DE, Polz MF. (2008). Rapid chemotactic response enables marine bacteria to exploit ephemeral microscale nutrient patches. Proc Natl Acad Sci USA 105: 4209-4214.
44. Taniguchi Y, Choi PJ, Li G-W, Chen H, Babu M, Hearn J et al. (2010). Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells. Science 329: 533-538.
45. Tyystjarvi T, Aro EM, Jansson C, Maenpaa. (1994). Changes of amino acid sequence in PEST-like area and QEEET motif affect degradation rate of D1 polypeptide in photosystem II. Plant Mol Biol 25: 517-526.
46. Vila-Costa M, Rinta-Kanto JM, Sun S, Sharma S, Poretsky R, Moran MA. (2010). Transcriptomic analysis of a marine bacterial community enriched with dimethylsulfoniopropionate. ISME J 4: 1410-1420.
47. Xu L, Chen H, Hu X, Zhang R, Zhang Z, Luo ZW. (2006). Average gene length is highly conserved in prokaryotes and eukaryotes and diverges only between the two kingdoms. Mol Biol Evol 23: 1107-1108.