HI BS Cường,
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So Much Diversity, Such Little Cells
Comparative yeast genomics reveals mechanisms of genome evolution
Nghiên cứu so sánh hệ gene ở nấm men giúp phát hiện các cơ chế tiến hóa của hệ gene.
Despite their small size, yeasts are undisputed titans (được công nhận là những người khổng lồ) in evolutionary terms. The genetic diversity of the 100,000 known species rivals (có thể so sánh với/không kém cạnh gì ) ?the entire chordate phylum, thanks to yeast's short lifespan, rapid reproduction, and small genomes.
Consequently, comparative genomic studies (nghiên cứu bộ gene theo hướng so sánh cấu trúc, trật tự bộ gene - so sánh genome) with yeast reveal a molecular diversity never before anticipated.
The three Hot Papers presented here describe yeast genome evolution in unprecedented detail (chi tiết chưa từng có), providing compelling evidence (bằng chứng mạnh mẽ) for whole-genome duplication (nhân đôi toàn bộ hệ gene) - a controversial theory ?(lý thuyết gây tranh cãi) ?first suggested in 1970.1 Because they provide insights (hiểu biết/tri thức) ?for large-scale evolutionary mechanisms (cơ chế tiến hoá ở quy mô lớn) for practically any genome, "these are landmark papers," says Andre Goffeau of the Catholic University of Louvain, Belgium.
Doubling Up To Evolve
Microbiologist Peter Philippsen and colleagues at the University of Basel, Switzerland, described the evolution of Saccharomyces cerevisiae by comparing it with Ashbya gossypii, a filamentous fungus (nấm sợi) sharing more than 90% homology. (sự tương đồng)2 Similarly, Manolis Kellis and colleagues at Massachusetts Institute of Technology and Cambridge University in Boston revealed compelling evidence of whole-genome duplication through comparison of S. cerevisiae to that of Kluyveromyces waltii, which diverged from (tách nhánh tiến hóa khỏi) S. cerevisiae prior to duplication.3 They showed that each region of K. waltii corresponds to two regions of S. cerevisiae.
Significantly, they also showed that 95% of cases of accelerated evolution (tiến hóa được tăng tốc/tăng tiến) ?involved only one member of a gene pair. "When you have a duplicated gene pair, you would think that both genes would diverge and acquire new functions," says Mark Johnston of Washington University, St. Louis. Instead, for some genes "one of the pair maintains its previous function, and the other diverges (tiến hóa thành chức năng khác) more rapidly." Such duplications, says Kellis, have proven widespread (phổ biến rộng). In S. cerevisiae, they identified 115 pairs in which one paralog (các protein có chức năng gần giống nhau được mã hóa trong cùng một hệ gene - có thể ?dịch là một copy của cặp gene ) evolved at least 50% faster than the other, with many genes involved in metabolism and cell growth. In phenotypic experiments, deleting the ancestral gene copy proved lethal in 18% of those tested. Deleting the evolved copy was never lethal.
The third Hot Paper,4 reported by Bernard Dujon of the Pasteur Institute in Paris, Jean-Luc Souciet of the Louis Pasteur University in Strasbourg, and colleagues, was the first to investigate genome evolution over an entire eukaryotic phylum. They sequenced the genomes of four distantly related yeast species: the human pathogen Candida glabrata, model organism Kluyveromyces lactis, salt-tolerant Debaryomyces hansenii, and the alkane-using Yarrowia lipolytica, and then compared them to S. cerevisiae. Their findings similarly described evidence for whole-genome duplications, in addition to segmental duplications, extensive gene losses, and tandem gene repeats (lặp gene theo kiểu nối đuôi nhau /trình tự lặp lại trước sau).
"The first major surprise was the large evolutionary range," says Dujon. "The second surprise was that in some branches, the mechanism of gene evolution was different from another." Thirdly, he adds, "The extent of gene loss was not anticipated." Most lost genes corresponded to specific metabolic pathways no longer required in given species' particular niches. C. glabrata's diminished genome (hệ gene suy giảm/suy thoái), a consequence of reductive evolution (tiến hóa theo hướng suy thoái), may reflect this yeast's adaptation as a human pathogen.
Comparisons Unbound
This five-organism cross-reference "is probably the best comparison of the relationship between yeast species," says Fred Sherman of the University of Rochester. "It gave a detailed analysis of the evolution of certain species and a clear picture of the pathway of evolution."
Much more can still be gleaned (khai thác) ?from yeast species. "We don't know if there are evolutionary gaps between clades (các loài có cùng tổ tiên)," says Dujon. Key molecular mechanisms of evolutionary history after duplication are still not clear.
YEASTS VERSUS CHORDATES: Though separate yeast species may not appear so different, the hemiascomycetes are every bit as diverse as entire vertebrate phylum on a genomic scale. Percent amino-acid identity with Saccharomyces cerevisiae or Homo sapiens reveal that yeasts display startling (đáng kinh ngạc) ?molecular diversity.
Presently, there are twenty-five complete yeast genomes representing different species, says Souciet. "Our future goal is to have a better understanding of yeast species that are very, very different to discover new kinds of organization (để phát hiện ra những cấu trúc mới trong hệ gene)."
Databases set up by Souciet and Dujon5,6 and Phippsen and colleagues7 should allow researchers to make those discoveries. Most recently, Souciet and colleagues have described their Genolevures online database, which contains data and tools for investigating four complete and ten partial yeast genomes.6 The database now provides truly complete chromosome sequence, including 25,000 protein-coding and tRNA genes, in silico analyses (phân tích trên máy tính), and a collection of conserved multispecies protein families (các họ protein có cùng chức năng ở nhiều loài) ?mapped to metabolic pathways. New genomes are being added this year.
Other groups are now setting their sights on yeast protein activities and interactions from various species. Philippsen says his group is currently focused on investigating proteins of S. cerevisiae and A. gossypii. "It turns out that several of the orthologous proteins (các protein tương ứng ở các loài được xác định bằng so sánh trình tự - các protein tương đồng) ?tested do not play the same cellular roles in both organisms."
Johnston says he and his colleagues have moved past the sequencing phase of such projects. In collaboration with Mike Snyder at Yale University, Johnston's team is now using protein arrays to identify DNA-binding proteins and to begin assembling a regulatory network (mạng lưới điều hòa). Kellis says he and his colleagues are studying network evolution in the context of whole genome duplication (trong khuôn khổ tiến hóa bằng cách nhân đôi toàn bộ hệ gene), now widely recognized in plant, tree, fungal, and vertebrate lineages.
Although simple, yeasts are quite evolved, and the basic methods to study the organism have given scientists a head start (lợi thế ban đầu) on understanding genome evolution of more complex organisms. Lund University microbiologist Jure Piskur says that the scope of these yeast studies has extended far beyond fungi. "The tools developed in these papers can be used for any other organism."
Bạn nào dịch ra rồi ta sẽ bàn thảo thêm về cái này.
Hôm qua tui lỡ tay xoá mất chủ đề này, mai mà laptop tui còn lưu lại nên kịp copy và paste thành chủ đề mới Sory BS Cường
So Much Diversity, Such Little Cells
Comparative yeast genomics reveals mechanisms of genome evolution
Nghiên cứu so sánh hệ gene ở nấm men giúp phát hiện các cơ chế tiến hóa của hệ gene.
Despite their small size, yeasts are undisputed titans (được công nhận là những người khổng lồ) in evolutionary terms. The genetic diversity of the 100,000 known species rivals (có thể so sánh với/không kém cạnh gì ) ?the entire chordate phylum, thanks to yeast's short lifespan, rapid reproduction, and small genomes.
Consequently, comparative genomic studies (nghiên cứu bộ gene theo hướng so sánh cấu trúc, trật tự bộ gene - so sánh genome) with yeast reveal a molecular diversity never before anticipated.
The three Hot Papers presented here describe yeast genome evolution in unprecedented detail (chi tiết chưa từng có), providing compelling evidence (bằng chứng mạnh mẽ) for whole-genome duplication (nhân đôi toàn bộ hệ gene) - a controversial theory ?(lý thuyết gây tranh cãi) ?first suggested in 1970.1 Because they provide insights (hiểu biết/tri thức) ?for large-scale evolutionary mechanisms (cơ chế tiến hoá ở quy mô lớn) for practically any genome, "these are landmark papers," says Andre Goffeau of the Catholic University of Louvain, Belgium.
Doubling Up To Evolve
Microbiologist Peter Philippsen and colleagues at the University of Basel, Switzerland, described the evolution of Saccharomyces cerevisiae by comparing it with Ashbya gossypii, a filamentous fungus (nấm sợi) sharing more than 90% homology. (sự tương đồng)2 Similarly, Manolis Kellis and colleagues at Massachusetts Institute of Technology and Cambridge University in Boston revealed compelling evidence of whole-genome duplication through comparison of S. cerevisiae to that of Kluyveromyces waltii, which diverged from (tách nhánh tiến hóa khỏi) S. cerevisiae prior to duplication.3 They showed that each region of K. waltii corresponds to two regions of S. cerevisiae.
Significantly, they also showed that 95% of cases of accelerated evolution (tiến hóa được tăng tốc/tăng tiến) ?involved only one member of a gene pair. "When you have a duplicated gene pair, you would think that both genes would diverge and acquire new functions," says Mark Johnston of Washington University, St. Louis. Instead, for some genes "one of the pair maintains its previous function, and the other diverges (tiến hóa thành chức năng khác) more rapidly." Such duplications, says Kellis, have proven widespread (phổ biến rộng). In S. cerevisiae, they identified 115 pairs in which one paralog (các protein có chức năng gần giống nhau được mã hóa trong cùng một hệ gene - có thể ?dịch là một copy của cặp gene ) evolved at least 50% faster than the other, with many genes involved in metabolism and cell growth. In phenotypic experiments, deleting the ancestral gene copy proved lethal in 18% of those tested. Deleting the evolved copy was never lethal.
The third Hot Paper,4 reported by Bernard Dujon of the Pasteur Institute in Paris, Jean-Luc Souciet of the Louis Pasteur University in Strasbourg, and colleagues, was the first to investigate genome evolution over an entire eukaryotic phylum. They sequenced the genomes of four distantly related yeast species: the human pathogen Candida glabrata, model organism Kluyveromyces lactis, salt-tolerant Debaryomyces hansenii, and the alkane-using Yarrowia lipolytica, and then compared them to S. cerevisiae. Their findings similarly described evidence for whole-genome duplications, in addition to segmental duplications, extensive gene losses, and tandem gene repeats (lặp gene theo kiểu nối đuôi nhau /trình tự lặp lại trước sau).
"The first major surprise was the large evolutionary range," says Dujon. "The second surprise was that in some branches, the mechanism of gene evolution was different from another." Thirdly, he adds, "The extent of gene loss was not anticipated." Most lost genes corresponded to specific metabolic pathways no longer required in given species' particular niches. C. glabrata's diminished genome (hệ gene suy giảm/suy thoái), a consequence of reductive evolution (tiến hóa theo hướng suy thoái), may reflect this yeast's adaptation as a human pathogen.
Comparisons Unbound
This five-organism cross-reference "is probably the best comparison of the relationship between yeast species," says Fred Sherman of the University of Rochester. "It gave a detailed analysis of the evolution of certain species and a clear picture of the pathway of evolution."
Much more can still be gleaned (khai thác) ?from yeast species. "We don't know if there are evolutionary gaps between clades (các loài có cùng tổ tiên)," says Dujon. Key molecular mechanisms of evolutionary history after duplication are still not clear.
YEASTS VERSUS CHORDATES: Though separate yeast species may not appear so different, the hemiascomycetes are every bit as diverse as entire vertebrate phylum on a genomic scale. Percent amino-acid identity with Saccharomyces cerevisiae or Homo sapiens reveal that yeasts display startling (đáng kinh ngạc) ?molecular diversity.
Presently, there are twenty-five complete yeast genomes representing different species, says Souciet. "Our future goal is to have a better understanding of yeast species that are very, very different to discover new kinds of organization (để phát hiện ra những cấu trúc mới trong hệ gene)."
Databases set up by Souciet and Dujon5,6 and Phippsen and colleagues7 should allow researchers to make those discoveries. Most recently, Souciet and colleagues have described their Genolevures online database, which contains data and tools for investigating four complete and ten partial yeast genomes.6 The database now provides truly complete chromosome sequence, including 25,000 protein-coding and tRNA genes, in silico analyses (phân tích trên máy tính), and a collection of conserved multispecies protein families (các họ protein có cùng chức năng ở nhiều loài) ?mapped to metabolic pathways. New genomes are being added this year.
Other groups are now setting their sights on yeast protein activities and interactions from various species. Philippsen says his group is currently focused on investigating proteins of S. cerevisiae and A. gossypii. "It turns out that several of the orthologous proteins (các protein tương ứng ở các loài được xác định bằng so sánh trình tự - các protein tương đồng) ?tested do not play the same cellular roles in both organisms."
Johnston says he and his colleagues have moved past the sequencing phase of such projects. In collaboration with Mike Snyder at Yale University, Johnston's team is now using protein arrays to identify DNA-binding proteins and to begin assembling a regulatory network (mạng lưới điều hòa). Kellis says he and his colleagues are studying network evolution in the context of whole genome duplication (trong khuôn khổ tiến hóa bằng cách nhân đôi toàn bộ hệ gene), now widely recognized in plant, tree, fungal, and vertebrate lineages.
Although simple, yeasts are quite evolved, and the basic methods to study the organism have given scientists a head start (lợi thế ban đầu) on understanding genome evolution of more complex organisms. Lund University microbiologist Jure Piskur says that the scope of these yeast studies has extended far beyond fungi. "The tools developed in these papers can be used for any other organism."
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