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DNA Research 2005 12(4):235-246; doi:10.1093/dnares/dsi008
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© The Author 2006. Kazusa DNA Research Institute
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Identity Elements of Archaeal tRNA

Bibekanand Mallick1, Jayprokas Chakrabarti1,2,*, Satyabrata Sahoo1, Zhumur Ghosh1 and Smarajit Das1

1Computational Biology Group (CBG), Theory Department, Indian Association for the Cultivation of Science Calcutta 700032 India
2Biogyan BF 286, Salt Lake, Calcutta 700064 India

Received 18 October 2004; revised 3 June 2005


   Abstract
Top
 Abstract
1. Introduction
 2. Materials and Methods
 3. Results and Discussion
 Acknowledgements
 References
 
Features unique to a transfer-RNA are recognized by the corresponding tRNA-synthetase. Keeping this in view we isolate the discriminating features of all archaeal tRNA. These are our identity elements. Further, we investigate tRNA-characteristics that delineate the different orders of Archaea.

Key words: Archaea; identity elements; AARS; tRNA secondary structure; tRNA tertiary structure; canonical introns; non-canonical introns; bulge–helix–bulge (BHB motif)


   1. Introduction
Top
 Abstract
 1. Introduction
2. Materials and Methods
 3. Results and Discussion
 Acknowledgements
 References
 
Transfer RNA (tRNA) genes form the single largest gene family. The yeast tRNAAla was the first to be sequenced.1Go tRNA consists of ~76 nucleotides. They are found in cytoplasm, as well as in mitochondria and chloroplast.2Go,3Go We deal with cytoplasmic tRNA genes of Archaea.4Go As of now, several powerful tRNA gene identification routines5Go–11Go are accessible. tRNA sequence databases12Go,13Go have grown. Archaeal tRNA genes have introns. Some introns occur at what are called canonical (i.e. between 37 and 38) sites. Introns appear at non-canonical sites (sites other than canonical) as well. The introns at non-canonical sites vary in size and number. These non-canonical introns make the detection of tRNA genes tricky. The present tRNA gene identification routines sometimes cannot sort out these introns. Consequently, some tRNA genes are embedded (http://arxiv.org/abs/q-bio/0507008), some missed or misidentified, e.g. Nanoarchaeum equitans. The present routines8Go,11Go do not get tRNATrp(CCA). Instead it gets a second copy of tRNASer(CGA) lying between nucleotides 151 992 and 152 081. We find this to be a misidentification (http://arxiv.org/abs/q-bio.GN/0504034). We infer that the nucleotides between 151 992 and 152 078 constitute tRNATrp(CCA) gene. It has a non-canonical intron, 13 bases long, between positions 30 and 31 of tRNATrp(CCA) gene. Again, the present routines miss tRNAiMet(CAT) gene in N. equitans; we find that it is located between nucleotides 35 249 and 35 429 with two non-canonical introns. For archaeal tRNA genes there are a few such cases. In this paper we address the identity elements (for recognition of cognate amino acids) in cytoplasmic tRNAs of Archaea.

In this study, we have analyzed 22 species of 12 orders of three phyla of Archaea [the sequences deposited at DDBJ (www.ddbj.nig.ac.jp/), NCBI, DOGAN (http://www.bio.nite.go.jp/dogan/Top/) and Microbial Genome Database (MGBD) at http://mbgd.genome.ad.jp/] including the recent phylum Nanoarchaeota and recently sequenced Picrophilus torridus. Out of these 22 species, 3 species whose sequencing are not yet completed, but the draft genome sequence is deposited by DOE Joint Genome Institute (JGI) (http://genome.ornl.gov/microbial/) are also taken for analysis. These three draft sequence are of M. barkeri and M. burtonii (Methanosarcinales) and F. acidarmanus (Thermoplasmatales).

Table 1 lists the Archaea and the abbreviations used to denote them. The other notations used in this paper are as follows: (i) tRNATrp(CCA) means tryptophan tRNA with anticodon, CCA; (ii) G1:C72 means base pairing between first nucleotide and 72nd nucleotide of tRNA. The abbreviation bp stands for base pair/base pairs. Semi-conserved bases are the ones that are conserved with but a few exceptions. 3D bp means three-dimensional base pairings. These are essential for tertiary structure.


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  		Various features of 22 species of Archaea.

 
The primary tRNA nucleotide chain is single stranded. This chain folds back onto itself to form the base paired secondary structure. This folded cloverleaf structure confers on tRNA some of its functions. The secondary structure of tRNA14Go has (i) Acceptor arm or A-arm: In this, the 5' and 3' ends of tRNA are base paired into a stem of 7 bp. (ii) DHU arm or D-Arm: Structurally a stem-loop, D-arm frequently contains the modified base dihydrouracil. (iii) Anticodon arm or AC-arm, made of a stem and a loop containing the anticodon. The canonical structure of AC-loop is essential for interactions with ribosomal A and P sites.15Go At 5' end of this loop is a pyrimidine base at 32, followed by an invariant U at 33. The anticodon triplet, at 34, 35, 36 is in the exposed loop region.13Go (iv) Extra arm, or V-arm: This arm is not always present. It is of variable length and is largely responsible for variations in the lengths of tRNAs. The classification of tRNAs into types I and II depends on the length of V-arm. (v) T-{psi}-C Arm or T-arm: This arm has conserved sequence of three ribonucleotides: ribothymidine, pseudouridine and cytosine. T-arm has stem–loop secondary structure and (vi) tRNA terminates with CCA at the 3' end.16Go For tRNA genes, CCA may not be present. In case CCA is absent in tRNA genes, it is added during the maturation to tRNA.

The attachment of cognate amino acids to their corresponding tRNA are catalyzed by aminoacyl-tRNA synthetase (AARS).17Go Accurate acylation of tRNA depends on two factors: a set of nucleotides in tRNA molecule (identity elements) responsible for proper identification by AARS18Go–21Go and competition between different synthetases for tRNAs.22Go–25Go Tertiary L-shape of tRNA facilitates its identification by AARS for aminoacylation.26Go L-shape comes about through the interactions between D-arm and T-arm. There are a few key features that maintain the L-shape of tRNA.27Go,28Go These interactions include Watson–Crick base pairing, Hoogsteen base pairing, and triple-helical base pairing. It is generally accepted that the major interactions maintaining the L-shape occur at the corner of the molecule where D- and T-loops meet. This region, called DT, contains several elements, including the reverse-Hoogsteen base pair U54:A58 and C55-mediated U-turn in T-loop, the inter-loop base pairs G18:C55 and G19:C56 and stack of four mutually intercalated purine bases A58–G18–R57–G19.29Go,30Go This intraloop U54:A58 is stacked on G53.C61 at the end of T stem and forces the two bases at positions 59 and 60 to loop out, forming a characteristic T-loop of five bases instead of seven. This characteristic T loop conformation is important for recognition by elongation factors.31Go We propose here all possible identity elements in tRNAs of Archaea for recognition of cognate amino acids. These are bases within tRNA sequences with which it would be possible to identify each of the tRNAs of individual archaeal species of different taxonomic groups.

From the 22 archaeal genomes, we sourced 1001 tRNA genes in total. We located tRNA genes using our in-house algorithm. Subsequently, we ran tRNAScan-SE and ARAGORN as additional checks.


   2. Materials and Methods
Top
 Abstract
 1. Introduction
 2. Materials and Methods
3. Results and Discussion
 Acknowledgements
 References
 
The archaeal genomes are obtained from NCBI and Genome Information Broker (http://gib.genes.nig.ac.jp/). Raw tRNA gene sequences are found by searching the different motifs present in the consensus sequence of different tRNAs genes of Archaea. At first we adopted the standard cloverleaf model1Go for studying the secondary structure of predicted tRNA genes of Archaea. In doing so, we got some false positives and a few tRNA genes were missed out. We then imposed constraints, unique to archaeal tRNA genes. A regular cloverleaf structure was searched in tRNA genes of the genomes by adopting archaeal tRNA gene features. The constraints of lengths of stems of regular tRNA A-arm, D-arm, AC-arm and T-arm are 7, 4, 5 and 5 bp, respectively. In a few cases, the length of D-arm and AC-arm are relaxed. In addition, parameters and constraints used in the search for cloverleaf tRNAs are the following: (i) T8 (except Y8 in M. kandleri), G18, R19, R53, Y55 and A58 are considered as conserved bases for Archaea. (ii) The lengths of introns and V-arm are allowed from 6 to 121 and up to 21, respectively. (iii) Positions optionally occupied in D-loop are 17, 17a, 20a and 20b. (iv) Canonical and non-canonical introns may or may not be present. Keeping these constraints, we were able to extract tRNA genes in all Archaea. (Number of tRNA genes obtained are given in Table 1). After getting the tRNA genes we ran the standard routines8Go,11Go to check for the secondary structure.


   3. Results and Discussion
Top
 Abstract
 1. Introduction
 2. Materials and Methods
 3. Results and Discussion
Acknowledgements
 References
 
Table 2 lists the conserved and semi-conserved bases/base pairs of various archaeal elongator tRNAs. In Table 3 we list the following identity elements.


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  		Conserved and semi-conserved bases/base pairs of various Archaeal elongator tRNAs.

 

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  		Identity elements of Archaeal tRNAs.

 
(i) tRNAAla. G3:U70 is a unique base pair in archaeal tRNAAla. Ala-RS specifically aminoacylates tRNAAla because of direct recognition of unique functional groups exposed on G3:U70. The G3:U70 pair contributes to tRNAAla identity by three mechanisms. First, the wobble pair presents a distinctive array of hydrogen bond donors and acceptors in major and minor grooves. Second, unusual structural features induced by the G3:U70 pair may influence Ala-RS binding to AC-stem and/or 3'-CCA end of tRNAAla. Third, G3:U70 may destabilize AC-end and favor the formation of an optimal active site geometry by induced fit.51Go These mechanisms are not mutually exclusive. The role of the functional groups in minor groove of A-stem on recognition and aminoacylation by Ala-RS has been extensively investigated.52Go A73 discriminator base could be another identity element.

(ii) tRNAArg. 1:72 of tRNAArg is conserved for Archaea, except A:U for tRNAArg(CCG) of MmGoe, Macet and Mbar. The third base of anticodon G36 or U36 and the second anticodon base C35 are arginine identities. A20 and the discriminator base A73 or G73 are identity elements as well. Nanoarchaea has U20 and A59. These unusual nucleotide positions may be identity elements for tRNAArg of Nanoarchaea.

(iii) tRNAAsn. Methanosarcinales have unique A10:U25 unlike G10:C25 in other Archaea. Similarly, all three Thermococcales (Pf, Paby and Phori) and Afulg, all hyperthermophiles, have U13:G22 in tRNAAsn. Other Archaea have C13:G22. For archaeal tRNAAsn, we find that C3:G70, G73 and G34, U35, U36 are the identity elements.

(iv) tRNAAsp. G4:C69 is characteristic of Crenarchaea which distinguishes it from Euryarchaea that have C4:G69 (exceptions: C4:G69 for Paero and U4:A69 in Pitor). Methanosarcinales differ at U2:G71 from C2:G71 in other Archaea. We surmise G6:C67 to be the identity determinant recognized by synthetase in addition to other identity elements of tRNAAsp in its anticodon, G34, U35 and C36.

(v) tRNACys. Thermoplasmales differs from other archaeal order at G2:C71 and A3:U70. Others have CG at these two positions. tRNACys(GCA) of Nanoarchaea differs from two other archaeal phyla at C10:G25. The two other phyla have G10:C25.

(vi) tRNAGln. C12:G23 in D-stem of Crenarchaea is a distinguishing feature of tRNAGln from G12:C23 of Euryarchaea. A at 73rd position is the discriminator base, with exception of tRNAGln(UUG) of Facid where G is the discriminator. The other identity elements of tRNAGln could be A1:U72 in addition to anticodon bases at 34th, 35th and 36th positions. The modified U base at 34th nucleotide could be the major identity element for the synthetase as in E.coli.53

(vii) tRNAGlu. The 3D bp 15:48 is GC, but tRNAGlu(UUC) of Mkan has CC at this position. The Sulfolobales and Desulfurococcales tRNAGlu differ from all Crenarchaea and Euryarchaea with G4:C69 from C4:G69 in all others. U34, U35 and C36 are identity elements for Archaea as in Escherichia coli. 54Go,55Go C5:G68 could be another identity element for archaeal tRNAGlu.

(viii) tRNAGly. Nanoarchaea is unique at 33rd site in its tRNAGly. It has pyrimidine C in tRNAGly(CCC) rather than U as in other two phyla. A73 acts as an identity element in addition to C35, C36.

(ix) tRNAHis. Methanococcales, Methanosarcinales and Thermoplasmales have G7:U66 not observed in other Archaea. Paero has UA at 11:24 unlike other Crenarchaea where it is CG. The discriminator base C73, the fourth unpaired base from the tRNA 3' end are the characteristic features of tRNAHis(GUG). These are the identity elements in addition to the anticodon. C50:G64 could be an additional identity element. G29:C41 could be a minor identity element as well.

(x) tRNAIle. Nanoarchaea unusually have tRNAIle(UAU) and tRNAIle (GAU) which differ from each other at 29:41, 31:39 and 49:65 with interchange of GC or CG. The first one (i.e. tRNAIle(UAU)) located between bases 225 624 and 225 716 has an intron unlike the second and it is the first tRNAIle(UAU) to be identified in Archaea. The two tRNAIle(GAU) of Macet are identical and have 3'-CCA arm. C27:G43 is presumably the identity element for tRNAIle(GAU). In addition, the anticodon and A73 are identity elements.

(xi) tRNALeu. MmGoe, Macet and Mburt have six tRNALeu with two identical copies of tRNALeu(GAG). The two copies of tRNALeu(GAG) gene of MmGoe are identical, but differ by CCA arm in one of them. A5:U68 is characteristic of tRNALeu of Thermoplasmales, except GC in tRNALeu(UAA). We surmise that G26:U44 is the discriminating factor (Table 3).

(xii) tRNALys. Hyperthermophilic Desulfurococcales have C32:C38; but other Archaea have CA. The discriminator bases G73 and U35 are the acceptor identities for tRNALys as in E coli. 56Go,57Go

(xiii) tRNAeMet (Elongator methionine tRNA). Two elongator tRNAMet(CAU) differ from one another at two positions. The first copy, tRNAeMet1(CAU) has CG at 2:71 and 3:70 of A-arm and the second tRNAeMet2(CAU) has GC at these positions. tRNAeMet1(CAU) of most of the Euryarchaea have canonical introns, but rare in its second copy. C34, A35 and U36 could be the identity elements in addition to the discriminator base A73.

(xiv) tRNAiMet(CAU) (Initiator methionine tRNA). Interestingly, Mmari, MmGoe, Macet have two copies of tRNAiMet(CAU). G28:C42 in Crenarchaeal tRNAiMet(CAU) distinguishes it from either CG or UG at this position in Euryarchaea. Mkan is again an exception in this respect where G28:C42 is present as in Crenarchaea. tRNAiMet of Halo is characterized by A7:U66 in contrast to G7:C66 in other Archaea.

Archaeal tRNAiMet(CAU) possesses unique sequence characteristics: (a) A1:U72 bp at the beginning of A-arm, (b) the three consecutive G and three C at the bottom of AC-stem forming GC bp in tRNAiMet(CAU) of Euryarchaea similar to bacteria.58Go Four consecutive GC bps in Crenarchaeal tRNAiMet unlike bacteria and eukaryotes. (c) G11:C24 in D- stem in contrast to C11:G24 in elongator tRNAs, (d) UA/AU bps at 51:63 in T-stem in contrast to GC for elongator tRNAs in all Archaea. The identity elements for tRNAiMet are listed in Table 3.

(xv) tRNAPhe(GAA). Crenarchaeal tRNAPhe(GAA) differs from Euryarchaea at C6:G67 against G6:C67 for Euryarchaea. Exception: halophilic tRNAPhe(GAA) are similar at 6:67 to Crenarchaea. C13:G22, we conjecture is an identity element. In addition to this, anticodon and A73 are identity elements.

(xvi) tRNAPro. Nanoarchaea has G10:C25. It is G10:U25 in Euryarchaea and either G10:C25 or G10:U25 in Crenarchaea. tRNAPro of Mther has A7:U66 in tRNAPro(UGG) which discriminate it from tRNAPro(UGG) of all other Archaea, where G7:C66 is observed. The three GC bps at 5' end of A-arm and A73 are the most probable regions for tRNA recognition for tRNAPro and G36 is a major determinant for aminoacylation, as reported for Mjan.59Go In addition to aminoacylation of tRNAPro by ProRS, this AARS has a dual function of aminoacylating tRNACys in Mjan, Mmari and Mther.60

(xvii) tRNASer. 6:67 is GC in Crenarchaea and Euryarchaea, but Nanoarchaea has CG. The present routines8Go,11Go get a second copy of tDNASer(CGA) in N. equitans lying between neclotides 151 992 and 152 081. We find that this is a misidentification and explained in detail in tRNATrp(CCA) section. We find for archaeal tRNASer G26:U44 can contribute to its recognition by Ser-RS. G73 and V-loop act as identity elements as in E. coli tRNASer.61Go

(xviii) tRNAThr. Thermococcales have conserved C12:G23 in tRNAThr(CGU) and tRNAThr(UGU) distinguishing these from other Euryarchaeal tRNAThr that have UA. For tRNAThr(UGU),31:39 bp differentiate between Crenarchaea and Euryarchaea; these have CG (exception: Paero has A:U) and AU respectively. U73, discriminator base is involved in recognition by Thr-RS in Archaea.62Go Second and third letters of anticodon, G35 and U36 are identity elements of archaeal Thr-RS as well.

(xix) tRNATrp(CCA). Tryptophan is a single codon amino acid and Archaea have at least one tRNATrp(CCA). The current standard routines8Go,11Go could not identify tRNATrp(CCA) in Nanoarchaea and we are able to identify it. The current standard routines identify the bases from 151 992 and 152 081 in Nanoarchaea as being tRNASer(CGA). We argue now that the bases between 151 992 and 152 081 are unlikely to be tRNASer(CGA). The reasons are as follows

  1. In tRNASer it is known that G26:U44, G73 and the elements in long V-arm are important for recognition by Ser-RS.63Go None of these recognition bases appear between 151 992 and 152 081. Instead we get G26:A44, A73 and a short V-arm.
  2. Variable arm for tRNASer is known to be long.61Go If we identify 151 992–152081 to be tRNASer(CGA), it is going to have a short V-arm missing out the elements important for its recognition by Ser-RS.
  3. However, the secondary structure generated from 151 992 to 152 078 have the following important positions G1, G2, G3, A21, T33, A73, G18:T55, G19:C56, T54:A58 and G30:C40 and anticodon CCA at 34, 35 and 36. These are known to be conserved in archaeal tRNATrp(CCA). Therefore, the range 151992–152078 is tRNATrp(CCA) gene. It has a non-canonical intron, 13 base-long between 30 and 31. It has BHB splicing motif as well.

U12:A23 in Crenarchaea distinguishes it from either GC or CG in Euryarchaea. The ninth base discriminates between Crenarchaea and Euryarchaea; the former have A and the latter have G. The anticodons C34, C35 and A36 are recognized by Trp-RS.64Go Additionally, A73 could also be the identity element.

(xx) tRNATyr. tRNATyr(GUA) of Archaea have characteristic base pairs at 31:39:GC bias in Crenarchaea and AU bias in Euryarchaea. The Methanosarcinales have unique AU, the first base pair of D-stem, that differentiate these from tRNATyr(GUA) of all other Archaea where GC is present. Base pair 2:71 is CG in general, but it is GC in Paero. G50:C64 of Nanoarchaea show identity with Crenarchaea and not with Euryarchaea where C50:G64 is present. The first base pair, CG in the A-arm is unique to tRNATyr(GUA) and absent in other tRNA. This base pair is an identity element of tRNATyr(GUA) for Tyr-RS in addition to the anticodons. This observation is experimentally supported in Mjan.65Go

(xxi) tRNAVal. MmGoe, Macet and Mbar have two identical copies of tRNAVal(GAC). UA is present at 4:69 in tRNAVal of Halo and in tRNAVal(GAC) of Mmari, but all other Archaea have CG. For archaeal tRNAVal, the second and third nucleotides of anticodon, A35, C36 and the conserved, unique base pair of U11:A24 could be the identity elements for recognition by Val-RS. Additionally, the discriminator base A73 could be another identity element.

Introns in archaeal tRNA genes
A unique feature of archaeal tRNA genes is their ability to occasionally host introns at locations other than the usual position within the anticodon loop (between bases 37 and 38) of tRNA genes. These unusually located introns in archaeal tRNA genes were observed in 1987.66Go Identification of introns outside the anticodon loop was made two years later.67Go Recently, introns were discovered in AC-loop between bases 32 and 33 in pre-tRNA-Pro (GGG) of Mther and many other locations in tRNA genes of Paero. Introns at canonical positions are located by existing software (tRNAScan-SE and ARAGORN). Identification of non-canonical introns in archaeal tRNA genes continues to be a challenge. We record in Table 4 the non-canonical introns in archaeal tRNA genes identified by our in-house algorithm.


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  		List of introns in tRNA genes from Archaea.

 


   Acknowledgements
Top
 Abstract
 1. Introduction
 2. Materials and Methods
 3. Results and Discussion
 Acknowledgements
References
 
We acknowledge the useful communications from Christian Marck.


   Footnotes
 
*To whom correspondence should be addressed. Tel. +91 33 24734971, ext. 281 (Off.). Fax. +91 33 24732805; E-mail: tpjc{at}iacs.res.in or biogyan{at}vsnl.net

Communicated by Michio Oishi


   References
Top
 Abstract
 1. Introduction
 2. Materials and Methods
 3. Results and Discussion
 Acknowledgements
 References
 

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