Protein rejects foreign DNA
Protein giúp tống xuất DNA ngoại lai
DNA-binding protein helps distinguish what genes Salmonella should incorporate
[Published 9th June 2006 06:49 PM GMT]
http://www.the-scientist.com/news/display/23609/
A DNA-binding protein (protein gắn lên/liên kết với DNA) apparently silences foreign DNA in Salmonella and perhaps other bacteria, helping regulate what they incorporate into (tích hợp/ gắn vào) their genomes, researchers reported in the June 8 online edition of Science.
This protein and other molecules could help protect against the potentially harmful effects (tác động bất lợi/có hại) of horizontal gene transfer (sự chuyển gene theo đường ngang) while leaving open the door for beneficial genes (gene có ích) to eventually get expressed, according to the paper. By helping bacteria distinguish between self- and foreign DNA (DNA của nó và/hoặc ngoại lai), they "might be viewed as a primitive immune system (hệ miễn dịch nguyên sơ)," study author Ferric Fang at University of Washington in Seattle told The Scientist.
The researchers investigated H-NS (histone-like nucleoid structuring protein - protein có cấu trúc nucleoid giống histone), which belongs to a family of small Gram-negative bacterial proteins that bind to DNA with relatively low sequence specificity (gắn lên DNA dựa trên tính đặc hiệu trình tự tương đối thấp)-- important to any potential role in suppressing (trấn áp/đàn áp) foreign DNA, which can be varied in sequence. Prior experiments showed H-NS can behave (cư xử/biểu hiện tính chất/tập tính/) as a transcriptional repressor and affect local supercoiling.
Fang and his colleagues identified genes H-NS regulates by comparing transcript levels (mức độ phiên mã) between wild-type and hns-null strains (chủng hoang dại và chủng bị loại bỏ gene hns) of Salmonella via cDNA microarray analysis. In hns-null mutants, they saw transcript levels of 178 open reading frames (ORFs) were reduced (bị giảm xuống) by more than three-fold, including ones for mobility and chemotaxis (tính di động/linh động và tính hóa hướng động), while 409 transcripts were more abundant (dồi dào, phong phú, sản lượng cao) , such as genes for virulence (các gene tạo nên tính độc/độc tính).
Of the 409 transcripts H-NS normally represses (ngăn chận, đàn áp), nearly 65% seem acquired from foreign sources (nguồn bên ngoài/ngoại lai), as they are not universally present (không hiện diện một cách phổ biến) in Salmonella's close relatives (loài tương cận/loài có quan hệ gần). They also possess significantly reduced levels of guanine and cytosine (GC). While the entire Salmonella genome's average GC content is 52.2%, transcripts displaying (bộc lộ/cho thấy/bày ra) three-fold or greater repression by H-NS had on average 46.8% GC. Chromatin immunoprecipitation (ChIP)-on-chip assays (phép thử dựa trên phương pháp tủa miễn dịch dùng trên đối tượng NST được thực hiện trên chip) showed 740 of 745 H-NS binding sites surveyed (các vị trí được khảo sát) were within 1,000 nucleotides of regions with 49% or less average GC content.
To see whether H-NS targeted (hướng tối mục tiêu) presumably foreign sequences lower in GC and richer in adenine and thymine (AT), the researchers recombined (kết hợp) a Helicobacter pylori gene with its promoter into a non-essential region (vùng không thiết yếu/quan trọng) of the Salmonella chromosome with an average GC content greater than 50% and no demonstrable interaction with H-NS. This gene, hp0226, was 39.7% GC.
Reverse transcriptase quantitative PCR (Q-PCR) analysis of transcript levels revealed wild-type strains repressed hp0226 expression more than 15-fold compared with hns-null mutants. Chromatin precipitation/Q-PCR found H-NS associated significantly with hp0226 but not with adjacent gene (gene liền kề) stm1033, which was 52.5% GC. This suggests H-NS binding silences AT-rich sequences.
The genome-wide average of GC content can vary from 25% to 75% between bacterial genera. "The use of AT content to distinguish 'self' from 'foreign' DNA may help to explain why different bacterial species retain (giữ/mang) characteristic AT/GC ratios," Fang said.
The roles of H-NS have been varied and confusing (gây bối rối) for years, and these findings provide "a platform to rationally tie many of these varied processes together, (cung cấp một cơ sở nến tảng để ràng buộc một cách vừa phải những quá trình thường hay biến đổi lại với nhau" Stanley Maloy at San Diego State University in California, who did not participate in this study, told The Scientist.
After hns-expressing bacteria incorporate foreign DNA into their genomes, Fang suggested H-NS silences it until counteracted (chống cự lại, trung hoà, làm mất tác dụng) by other proteins such as SlyA or Ler. Investigators should analyze how other molecules counter H-NS, such as competition with H-NS, changing the structure of DNA to lower H-NS affinity (ái lực) for it, or physical interaction (tương tác vật lý) with H-NS, Linda Kenney at the University of Illinois at Chicago, also not a co-author, told The Scientist.
The primary sequence of H-NS primary sequence is poorly conserved outside of enteric bacteria and close relatives such as Vibrio bacteria, which include cholera. Future experiments should uncover the mechanisms underlying H-NS recognition (nhận diện) of AT-rich sequences, to perhaps discover proteins in other bacteria with similar structures and roles, Fang said. "It will be interesting to determine whether AT-rich bacteria have another type of protein that recognizes and silences GC-rich DNA," he added.
H-NS has a higher affinity for curved DNA. Experiments should investigate growth conditions that might affect DNA curvature and see whether H-NS completely silences genes or just down-regulates them, Charles Dorman at Trinity College Dublin, who did not participate in this study, told The Scientist.
Charles Q. Choi
cchoi@the-scientist.com
Links within this article
W.W. Navarre et al. "Selective silencing of foreign DNA with low GC content by the H-NS protein in Salmonella enterica Sv. Typhimurium." Science, published online June 8, 2006.
www.sciencemag.org
Ferric Fang
depts.washington.edu/fanglab/
B. Maher. "The nucleosome untangled." The Scientist, May 1, 2006.
www.the-scientist.com/article/display/23392/
J. M. Perkel, "Chromatin precipitation," The Scientist, May 1, 2006.
www.the-scientist.com/article/display/23389/
Stanley Maloy
www.the-scientist.com/article/display/22639/
Linda Kenney
www.uic.edu/depts/mcmi/faculty/kenney.html
K. Hopkin. "How bacteria talk." The Scientist, June 1, 2006.
www.the-scientist.com/article/display/23546/
Charles Dorman
www.tcd.ie/Microbiology/page221.html
Comment on this news story
Protein giúp tống xuất DNA ngoại lai
DNA-binding protein helps distinguish what genes Salmonella should incorporate
[Published 9th June 2006 06:49 PM GMT]
http://www.the-scientist.com/news/display/23609/
A DNA-binding protein (protein gắn lên/liên kết với DNA) apparently silences foreign DNA in Salmonella and perhaps other bacteria, helping regulate what they incorporate into (tích hợp/ gắn vào) their genomes, researchers reported in the June 8 online edition of Science.
This protein and other molecules could help protect against the potentially harmful effects (tác động bất lợi/có hại) of horizontal gene transfer (sự chuyển gene theo đường ngang) while leaving open the door for beneficial genes (gene có ích) to eventually get expressed, according to the paper. By helping bacteria distinguish between self- and foreign DNA (DNA của nó và/hoặc ngoại lai), they "might be viewed as a primitive immune system (hệ miễn dịch nguyên sơ)," study author Ferric Fang at University of Washington in Seattle told The Scientist.
The researchers investigated H-NS (histone-like nucleoid structuring protein - protein có cấu trúc nucleoid giống histone), which belongs to a family of small Gram-negative bacterial proteins that bind to DNA with relatively low sequence specificity (gắn lên DNA dựa trên tính đặc hiệu trình tự tương đối thấp)-- important to any potential role in suppressing (trấn áp/đàn áp) foreign DNA, which can be varied in sequence. Prior experiments showed H-NS can behave (cư xử/biểu hiện tính chất/tập tính/) as a transcriptional repressor and affect local supercoiling.
Fang and his colleagues identified genes H-NS regulates by comparing transcript levels (mức độ phiên mã) between wild-type and hns-null strains (chủng hoang dại và chủng bị loại bỏ gene hns) of Salmonella via cDNA microarray analysis. In hns-null mutants, they saw transcript levels of 178 open reading frames (ORFs) were reduced (bị giảm xuống) by more than three-fold, including ones for mobility and chemotaxis (tính di động/linh động và tính hóa hướng động), while 409 transcripts were more abundant (dồi dào, phong phú, sản lượng cao) , such as genes for virulence (các gene tạo nên tính độc/độc tính).
Of the 409 transcripts H-NS normally represses (ngăn chận, đàn áp), nearly 65% seem acquired from foreign sources (nguồn bên ngoài/ngoại lai), as they are not universally present (không hiện diện một cách phổ biến) in Salmonella's close relatives (loài tương cận/loài có quan hệ gần). They also possess significantly reduced levels of guanine and cytosine (GC). While the entire Salmonella genome's average GC content is 52.2%, transcripts displaying (bộc lộ/cho thấy/bày ra) three-fold or greater repression by H-NS had on average 46.8% GC. Chromatin immunoprecipitation (ChIP)-on-chip assays (phép thử dựa trên phương pháp tủa miễn dịch dùng trên đối tượng NST được thực hiện trên chip) showed 740 of 745 H-NS binding sites surveyed (các vị trí được khảo sát) were within 1,000 nucleotides of regions with 49% or less average GC content.
To see whether H-NS targeted (hướng tối mục tiêu) presumably foreign sequences lower in GC and richer in adenine and thymine (AT), the researchers recombined (kết hợp) a Helicobacter pylori gene with its promoter into a non-essential region (vùng không thiết yếu/quan trọng) of the Salmonella chromosome with an average GC content greater than 50% and no demonstrable interaction with H-NS. This gene, hp0226, was 39.7% GC.
Reverse transcriptase quantitative PCR (Q-PCR) analysis of transcript levels revealed wild-type strains repressed hp0226 expression more than 15-fold compared with hns-null mutants. Chromatin precipitation/Q-PCR found H-NS associated significantly with hp0226 but not with adjacent gene (gene liền kề) stm1033, which was 52.5% GC. This suggests H-NS binding silences AT-rich sequences.
The genome-wide average of GC content can vary from 25% to 75% between bacterial genera. "The use of AT content to distinguish 'self' from 'foreign' DNA may help to explain why different bacterial species retain (giữ/mang) characteristic AT/GC ratios," Fang said.
The roles of H-NS have been varied and confusing (gây bối rối) for years, and these findings provide "a platform to rationally tie many of these varied processes together, (cung cấp một cơ sở nến tảng để ràng buộc một cách vừa phải những quá trình thường hay biến đổi lại với nhau" Stanley Maloy at San Diego State University in California, who did not participate in this study, told The Scientist.
After hns-expressing bacteria incorporate foreign DNA into their genomes, Fang suggested H-NS silences it until counteracted (chống cự lại, trung hoà, làm mất tác dụng) by other proteins such as SlyA or Ler. Investigators should analyze how other molecules counter H-NS, such as competition with H-NS, changing the structure of DNA to lower H-NS affinity (ái lực) for it, or physical interaction (tương tác vật lý) with H-NS, Linda Kenney at the University of Illinois at Chicago, also not a co-author, told The Scientist.
The primary sequence of H-NS primary sequence is poorly conserved outside of enteric bacteria and close relatives such as Vibrio bacteria, which include cholera. Future experiments should uncover the mechanisms underlying H-NS recognition (nhận diện) of AT-rich sequences, to perhaps discover proteins in other bacteria with similar structures and roles, Fang said. "It will be interesting to determine whether AT-rich bacteria have another type of protein that recognizes and silences GC-rich DNA," he added.
H-NS has a higher affinity for curved DNA. Experiments should investigate growth conditions that might affect DNA curvature and see whether H-NS completely silences genes or just down-regulates them, Charles Dorman at Trinity College Dublin, who did not participate in this study, told The Scientist.
Charles Q. Choi
cchoi@the-scientist.com
Links within this article
W.W. Navarre et al. "Selective silencing of foreign DNA with low GC content by the H-NS protein in Salmonella enterica Sv. Typhimurium." Science, published online June 8, 2006.
www.sciencemag.org
Ferric Fang
depts.washington.edu/fanglab/
B. Maher. "The nucleosome untangled." The Scientist, May 1, 2006.
www.the-scientist.com/article/display/23392/
J. M. Perkel, "Chromatin precipitation," The Scientist, May 1, 2006.
www.the-scientist.com/article/display/23389/
Stanley Maloy
www.the-scientist.com/article/display/22639/
Linda Kenney
www.uic.edu/depts/mcmi/faculty/kenney.html
K. Hopkin. "How bacteria talk." The Scientist, June 1, 2006.
www.the-scientist.com/article/display/23546/
Charles Dorman
www.tcd.ie/Microbiology/page221.html
Comment on this news story
