From DNA sequence to biological function

Genome sequencing is leading to the discovery of new genes at a rate 50–100 times greater than that achieved by classical genetics, but the biological function of almost half of these genes is completely unknown. In order fully to exploit genome sequence data, a systematic approach to the discovery of gene function is required. Possible strategies are discussed here in the context of functional analysis in the yeast Saccfiaromyces cerevisiae, a model eukaryote whose genome sequence will soon be completed.

[1]  Reinhart Heinrich,et al.  A linear steady-state treatment of enzymatic chains. General properties, control and effector strength. , 1974, European journal of biochemistry.

[2]  S. Cohen,et al.  Lactose genes fused to exogenous promoters in one step using a Mu-lac bacteriophage: in vivo probe for transcriptional control sequences. , 1979, Proceedings of the National Academy of Sciences of the United States of America.

[3]  D. Kaback,et al.  Improved methods for the formation and stabilization of R-loops. , 1979, Nucleic Acids Research.

[4]  R. Rothstein.  One-step gene disruption in yeast. , 1983, Methods in enzymology.

[5]  L. C. Robinson,et al.  RAS2 of Saccharomyces cerevisiae is required for gluconeogenic growth and proper response to nutrient limitation. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[6]  J R Johnston,et al.  Genealogy of principal strains of the yeast genetic stock center. , 1986, Genetics.

[7]  M. Goebl,et al.  Most of the yeast genomic sequences are not essential for cell growth and division , 1986, Cell.

[8]  Steven Hahn,et al.  Yeast HAP2 and HAP3 activators both bind to the CYC1 upstream activation site, UAS2, in an interdependent manner , 1987, Cell.

[9]  P. Warner,et al.  Plantacin B, a bacteriocin produced by Lactobacillus plantarum NCDO 1193 , 1988 .

[10]  K. Isono,et al.  Chromosome III of Saccharomyces cerevisiae: An ordered clone bank, a detailed restriction map and analysis of transcripts suggest the presence of 160 genes , 1990, Yeast.

[11]  A. Kerlavage,et al.  Complementary DNA sequencing: expressed sequence tags and human genome project , 1991, Science.

[12]  S. Fields,et al.  The two-hybrid system: a method to identify and clone genes for proteins that interact with a protein of interest. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[13]  D. Chadwick,et al.  Secondary metabolites: their function and evolution. , 1992 .

[14]  B. Dujon,et al.  The complete DNA sequence of yeast chromosome III , 1992, Nature.

[15]  R. Staden,et al.  The C. elegans genome sequencing project: a beginning , 1992, Nature.

[16]  Robert H. White,et al.  Cysteine desulfurase activity indicates a role for NIFS in metallocluster biosynthesis. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[17]  C Ouzounis,et al.  Homology of the NifS family of proteins to a new class of pyridoxal phosphate‐dependent enzymes , 1993, FEBS letters.

[18]  E. Craig,et al.  Heat shock proteins: molecular chaperones of protein biogenesis , 1993, Microbiological reviews.

[19]  C. Dean,et al.  Genes and genomes: Towards construction of an overlapping YAC library of the Arabidopsis thaliana genome , 1993 .

[20]  M V Olson,et al.  The human genome project. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[21]  D. Sun,et al.  Cloning, nucleotide sequence, and regulation of the Bacillus subtilis nadB gene and a nifS-like gene, both of which are essential for NAD biosynthesis , 1993, Journal of bacteriology.

[22]  P. Christen,et al.  Homology of pyridoxal-5'-phosphate-dependent aminotransferases with the cobC (cobalamin synthesis), nifS (nitrogen fixation), pabC (p-aminobenzoate synthesis) and malY (abolishing endogenous induction of the maltose system) gene products. , 1993, European journal of biochemistry.

[23]  D. Hopwood,et al.  The chromosomal DNA of Streptomyces lividans 66 is linear , 1993, Molecular microbiology.

[24]  K. Isono,et al.  Correlation between observed transcripts and sequenced ORFs of chromosome III of Saccharomyces cerevisiae. , 1993, Nucleic acids research.

[25]  J. Hammond.  2 – Brewer’s Yeasts , 1993 .

[26]  O. Ozier-Kalogeropoulos,et al.  A simple and efficient method for direct gene deletion in Saccharomyces cerevisiae. , 1993, Nucleic acids research.

[27]  P A Quant.  Experimental application of top-down control analysis to metabolic systems. , 1993, Trends in biochemical sciences.

[28]  Co-chairman's remarks: the human genome project and cancer. , 1993, Gene.

[29]  M. Aigle,et al.  Complete DNA sequence of yeast chromosome II. , 1994, The EMBO journal.

[30]  B. Daignan-Fornier,et al.  A genetic screen to isolate genes regulated by the yeast CCAAT‐box binding protein Hap2p , 1994, Yeast.

[31]  J. Todd,et al.  A genome-wide search for human type 1 diabetes susceptibility genes , 1994, Nature.

[32]  On the pulse of genetic cardiology , 1994, Nature Genetics.

[33]  C. Sensen,et al.  Complete DNA sequence of yeast chromosome XI , 1994, Nature.

[34]  P. Ross-Macdonald,et al.  Large-scale analysis of gene expression, protein localization, and gene disruption in Saccharomyces cerevisiae. , 1994, Genes & development.

[35]  W. Bodmer,et al.  Genetic steps in colorectal cancer , 1994, Nature Genetics.

[36]  B. Brenner,et al.  Hypertension: Pathophysiology, Diagnosis, and Management , 1994 .

[37]  Jonathan A. Cooper,et al.  Complete nucleotide sequence of Saccharomyces cerevisiae chromosome VIII. , 1994, Science.

[38]  M S Boguski,et al.  Genes conserved in yeast and humans. , 1994, Human molecular genetics.

[39]  S. Oliver,et al.  A Lactobacillus nifS-like gene suppresses an Escherichia coli transaminase B mutation. , 1994, Biochimie.

[40]  R. Durbin,et al.  2.2 Mb of contiguous nucleotide sequence from chromosome III of C. elegans , 1994, Nature.

[41]  E. Kirkness,et al.  cDNA sequencing: a means of understanding cellular physiology. , 1994, Current opinion in biotechnology.

[42]  P. Philippsen,et al.  New heterologous modules for classical or PCR‐based gene disruptions in Saccharomyces cerevisiae , 1994, Yeast.

[43]  R. Fleischmann,et al.  Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. , 1995, Science.

[44]  S. Kantha.  Einstein and Lorentz , 1995, Nature.

[45]  Takuji Sasaki,et al.  Rice genome analysis by integration of sequencing and mapping data , 1995 .

[46]  The Bacillus subtilis genome project: aims and progress. , 1995, Trends in biotechnology.

[47]  H. Bussey,et al.  The nucleotide sequence of chromosome I from Saccharomyces cerevisiae. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[48]  R. Fleischmann,et al.  Frequency and distribution of DNA uptake signal sequences in the Haemophilus influenzae Rd genome. , 1995, Science.

[49]  M. Yamazaki,et al.  Analysis of the nucleotide sequence of chromosome VI from Saccharomyces cerevisiae , 1995, Nature Genetics.

[50]  J. Witte,et al.  Genetic dissection of complex traits. , 1994, Nature genetics.

[51]  Douglas E. Bassett,et al.  Yeast genes and human disease , 1996, Nature.